chr15-74882685-A-G

Variant names:

• chr15-74882685-A-G
• rs6495126

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.671 in 151,966 control chromosomes in the GnomAD database, including 34,514 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101941 AN: 151846 Hom.: 34475 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.672

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.671 AC: 102028 AN: 151966 Hom.: 34514 Cov.: 31 AF XY: 0.669 AC XY: 49699 AN XY: 74274

African (AFR) AF: 0.608 AC: 25203 AN: 41424

American (AMR) AF: 0.718 AC: 10954 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2265 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4571 AN: 5166

South Asian (SAS) AF: 0.650 AC: 3129 AN: 4816

European-Finnish (FIN) AF: 0.645 AC: 6802 AN: 10548

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46776 AN: 67964

Other (OTH) AF: 0.674 AC: 1426 AN: 2116

Alfa AF: 0.685 Hom.: 61402

Bravo AF: 0.681

Asia WGS AF: 0.798 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.18
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6495126; hg19: chr15-75175026; COSMIC: COSV53421904;